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Gene order in Prokaryotes: conservation and implications

  • Chapter
Molecules in Time and Space

Summary

Genes in Prokaryotes are often organised in operons, groups of contiguous genes that function as single transcription units, or clusters, groups of contiguous genes subject to complex regulation that code for several transcripts. Several models suggest that the grouping of genes in operons or clusters provides physiological and genetic advantages that positively select their formation and maintenance. However, gene order along the chromosome is an evolutionary trait that is lost relatively quickly, since frequent chromosomal reorganisations and acquisition of foreign DNA shuffle the genetic material. As result, operons are generally conserved only among closely related species and widely conserved operons are scarce, although gene neighbourhood may be a more conserved property. Interestingly, the conservation of operons, gene clusters or neighbourhoods can be used as indicator of functional relations between gene products.

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References

  • Apic, G., Gough, J. and Teichmann S. (2001) Domain combination in archeal, eubacterial, and eukaryotic proteomes. J.Mol. Biol. 310, 311–325.

    Article  PubMed  CAS  Google Scholar 

  • Bader, G. D., Betel, D. and Hogue, C.W. (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250.

    Article  PubMed  CAS  Google Scholar 

  • Bashton, M. and Cothia, C. (2002) The geometry of domain combinations in proteins. J. Mol. Biol. 315, 927–939.

    Article  PubMed  CAS  Google Scholar 

  • Baumberg, S. (ed) (1999) Prokaryotic gene expression. Oxford University Press, New York.

    Google Scholar 

  • Beckwith, J. (1996) The Operon: an Historical Account. In Escherichia coli and Salmonella Typhimurium. Cellular and Molecular Biology, 2nd ed. (Neidhardt F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B,. Reznikoff W., Schaechter M., Umbarger H.E. and Riley M., Eds.), ASM Press, Washington D.C. Chap 78: pp 1227–1231.

    Google Scholar 

  • Blake, J. A. and Harris, M. (2003) The Gene Ontology Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. In Current Protocols in Bioinformatic (A.D. Baxevanis, D.B. Davison, R. Page, G. Stormo and L. Stein, Eds.). Wiley and Sons, Inc., New York.

    Google Scholar 

  • Bockhorst, J., Craven, M., Page, D., Shavlik, J. and Glasner J. (2003a) A Bayesian network approach to operon prediction. Bioinformatics 19, 1227–1235.

    Article  PubMed  CAS  Google Scholar 

  • Bockhorst, J., Qiu, Y., Glasner, J., Liu, M., Blattner, F. and Craven, M. (2003b) Predicting bacterial transcription units using sequence and expression data. Bioinformatics 19(Suppl 1), I34–I43.

    PubMed  Google Scholar 

  • Burton, Z. F., Gross, C. A., Watanabe, K. K. and Burgess, R.R. (1983) The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Cell 32, 335–349.

    Article  PubMed  CAS  Google Scholar 

  • Cases, I., de Lorenzo, V. and Ouzounis, C.A. (2003) Transcription regulation and environmental adaptation in Bacteria. Trends Microbiol. 11, 248–253.

    Article  PubMed  CAS  Google Scholar 

  • Cherry, J. L. (2003) Genome size and operon content. J. Theor. Biol. 221, 401–410.

    Article  PubMed  CAS  Google Scholar 

  • Conant, G. C. and Wagner, A. (2003) Convergent evolution of gene circuits. Nat. Genet. 34, 264–266.

    Article  PubMed  CAS  Google Scholar 

  • Craven, M., Page, D., Shavlik, J., Bockhorst, J. and Glasner, J. (2000) A probabilistic learning approach to whole-genome operon prediction. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 116–127.

    PubMed  CAS  Google Scholar 

  • Dandekar, T., Snel, B., Huynen, M. and Bork P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328.

    Article  PubMed  CAS  Google Scholar 

  • de Daruvar, A., Collado-Vides, J. and Valencia, A. (2002) Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J. Mol. Evol. 55, 211–221.

    PubMed  Google Scholar 

  • Demerec, M. and Hartman, P. (1959) Annu. Rev. Microbiol. 13: 377–406.

    Article  Google Scholar 

  • Enright, A. J., Iliopoulos, I., Kyrpides, N. C. and Ouzounis, C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature. 402, 86–90.

    PubMed  CAS  Google Scholar 

  • Enright, A. J. and Ouzounis, C.A. (2001) Functional associations of proteins in entire genomes via exhaustive detection of gene fusion. Genome Biology. 2, 341–347.

    Article  Google Scholar 

  • Ermolaeva, M. D, White, O. and Salzberg, S. L. (2001) Prediction of operons in microbial genomes. Nucleic Acids Res. 29, 1216–1221.

    Article  PubMed  CAS  Google Scholar 

  • Gavin, A. C., Bösche, M., Krause, R., Grandi, P., Marzioch. M., et al. (2002) Functional organisation of the yeast proteome by systematic analysis of protein complexes. Nature. 415, 141–147.

    Article  PubMed  CAS  Google Scholar 

  • Ge, H., Liu, Z., Church, G. M. and Vidal, M. (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 29, 482–486.

    Article  PubMed  CAS  Google Scholar 

  • Glansdorff, N. (1999) On the origin of operons and their possible role in evolution toward thermophily. J. Mol. Evol. 49, 432–438.

    PubMed  CAS  Google Scholar 

  • Gogarten, J. P., Doolittle, W.F. and Lawrence, J. G. (2002) Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226–2238.

    PubMed  CAS  Google Scholar 

  • Grigoriev, A. (2001) A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 29, 3513–3519.

    Article  PubMed  CAS  Google Scholar 

  • Guelzim, N., Bottani, S., Bourgine, S., Képés, F. (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31, 60–63.

    Article  PubMed  CAS  Google Scholar 

  • Hacker, J., Blum-Oehler, G., Muhldorfer, I. and Tschape, H. (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23, 1089–1097.

    Article  PubMed  CAS  Google Scholar 

  • Henkin, T. M. and Yanofsky, C. (2002) Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24, 700–707.

    Article  PubMed  CAS  Google Scholar 

  • Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415, 123–124.

    Article  Google Scholar 

  • Huerta, A. M., Salgado, H., Thieffry, D. and Collado-Vides, J. (1998) RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26, 55–59.

    Article  PubMed  CAS  Google Scholar 

  • Huynen, M., Snel, B., Lathe, W. 3 rd and Bork, P. (2000a) Exploitation of gene context. Curr. Opin. Struct. Biol. 10, 366–370.

    Article  PubMed  CAS  Google Scholar 

  • Huynen, M., Snel, B., Lathe, W. 3 rd and Bork, P. (2000b) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10, 1204–1210.

    Article  PubMed  CAS  Google Scholar 

  • Huynen, M. A. and Bork, P. (1998) Measuring genome evolution. Proc. Natl. Acad. Sci. USA. 95, 5849–5856.

    Article  PubMed  CAS  Google Scholar 

  • Huynen, M. A., Snel, B., von Mering, C. and Bork, P. (2003) Function prediction and protein networks. Curr. Opin. Cell. Biol. 15, 191–198.

    Article  PubMed  CAS  Google Scholar 

  • Itoh, T., Takemoto, K., Mori, H. and Gojobori, T. (1999) Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16, 332–346.

    PubMed  CAS  Google Scholar 

  • Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., el al. (2000) Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA. 97, 1143–1147.

    PubMed  CAS  Google Scholar 

  • Jacob, F. (1966) Genetics of the Bacterial Cell. Science. 152, 1470–1478.

    PubMed  CAS  Google Scholar 

  • Jacob, F., Perrin, D., Sánchez, C. and Monod, J. (1960) L’Operon: groupe des gènes à expression cordonée par un operateur. C. R. Seances Acad. Sci. 250, 1727–1729.

    CAS  Google Scholar 

  • Jacob, F. and Monod, J. (1961a) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356.

    Article  PubMed  CAS  Google Scholar 

  • Jacob, F. and Monod, J. (1961b) On the regulation of gene activity. Cold Spring Harb. Symp. Quant. Biol. 26, 193–211.

    CAS  Google Scholar 

  • Jansen, R., Greenbaum, D. and Gerstein, M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37–46.

    Article  PubMed  CAS  Google Scholar 

  • Jeong, H., Mason, S.P., Barabasi, A. L. and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41–42.

    Article  PubMed  CAS  Google Scholar 

  • Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. and Barabasi, A. L. (2000) The large-scale organization of metabolic networks. Nature 407, 651–654.

    PubMed  CAS  Google Scholar 

  • Juan, D., Devos, D., Pazos, F., Ouzounis, C., Blaschke, C. and Valencia, A. (2003) Reconstruction of the E. coli interactome. Small is still beautiful. Submitted for publication.

    Google Scholar 

  • Kanehisha, M., Goto, S., Kavashima, S. and Nakaya, A. (2002) The KEGG databases at GenomeNet. Nucleic Acid Res. 30, 42–46.

    Google Scholar 

  • Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Collado-Vides, J., Paley, S. M., Pellegrini-Toole, A., Bonavides, C., Gama-Castro, S. (2002) The EcoCyc Database. Nucleic Acids Res. 30, 56–58.

    PubMed  CAS  Google Scholar 

  • Korbel, J. O., Snel, B., Huynen, M. A. and Bork, P. (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18, 158–162.

    Article  PubMed  CAS  Google Scholar 

  • Landick, R., Turnbough, Jr. C. L. and Yanofsky, C, (1996) Transcription Attenuation. In Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology, 2nd ed. (Neidhardt, F. C., Curtiss III, R., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik B, Reznikoff, W., Schaechter, M., Umbarger, H. E. and Riley, M., Eds). ASM Press, Washington D.C. Chap 81: pp 1263–1286.

    Google Scholar 

  • Lathe, W. C. 3rd, Snel, B. and Bork, P. (2000) Gene context conservation of a higher order than operons. Trends Biochem. Sci. 25, 474–479.

    Article  PubMed  CAS  Google Scholar 

  • Lawrence, J. G. (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9, 642–648.

    Article  PubMed  CAS  Google Scholar 

  • Lawrence, J. G. (1997) Selfish operons and speciation by gene transfer. Trends Microbiol. 5, 355–359.

    Article  PubMed  CAS  Google Scholar 

  • Lawrence, J. G. and Ochman H. (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. U S A. 95, 9413–9417.

    Article  PubMed  CAS  Google Scholar 

  • Lawrence, J. G. and Roth, J. R. (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–1860.

    PubMed  CAS  Google Scholar 

  • Maas, W. K. (1964) Studies on the Mechanism of Repression of Arginine Biosynthesis in Escherichia coli II. Dominance of Repressibility in Diploids. J. Mol. Biol. 8, 365–370.

    CAS  PubMed  Google Scholar 

  • Madan Babu, M. and Teichmann, S. (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31, 1234–1244.

    Article  PubMed  CAS  Google Scholar 

  • Marcotte, E. M., Pellegrini, M., Ho-Leung, N., Rice, D. W., Yeates, T. O. and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science. 285, 751–753.

    Article  PubMed  CAS  Google Scholar 

  • Martínez-Antonio, A. and Collado-Vides J. (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6, 482–489.

    PubMed  Google Scholar 

  • Mellor, J. C., Yanai, I., Clodfelter, K. H., Mintseris, J. and DeLisi, C. (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 30, 306–309.

    Article  PubMed  CAS  Google Scholar 

  • Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K. et al. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30, 31–34.

    Article  PubMed  CAS  Google Scholar 

  • Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. and Alon U. (2002) Networks motifs: simple building blocks of complex networks. Science. 298, 824–827.

    Article  PubMed  CAS  Google Scholar 

  • Moreno-Hagelsieb, G. and Collado-Vides J. (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics. 18(Suppl 1), S329–336.

    PubMed  Google Scholar 

  • Mushegian, A. R. and Koonin, E. V. (1996) Gene order is not conserved in bacterial evolution. Trends. Genet. 12, 289–290.

    Article  PubMed  CAS  Google Scholar 

  • Okuda, S., Kawashima, S. and Kanehisa, M. (2002) Database of operons in Bacillus subtilis. Genome Informatics 13, 496–497.

    CAS  Google Scholar 

  • Overbeek, R., Fonstein, M., D’Souza, M., Pusch, G. D., and Maltsev N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA. 96, 2896–2901.

    Article  PubMed  CAS  Google Scholar 

  • Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271, 511–523.

    Article  PubMed  CAS  Google Scholar 

  • Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of proteinprotein interaction. Protein Eng. 14, 609–614.

    PubMed  CAS  Google Scholar 

  • Pazos, F. and Valencia A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 47, 219–227.

    Article  PubMed  CAS  Google Scholar 

  • Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. and Yates, T. O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad Sci. USA 96, 4285–4288.

    Article  PubMed  CAS  Google Scholar 

  • Pérez-Rueda, E. and Collado-Vides, J. (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28, 1838–1847.

    PubMed  Google Scholar 

  • Remm, M., Storm, C. E. V. and Sonnhammer, E. L. L. (2001) Automatic Clustering of Orthologs and In-paralogs from Pairwise Species Comparisons. J. Mol. Biol., 314, 1041–1052.

    Article  PubMed  CAS  Google Scholar 

  • Riley, M. (1997) Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucleic Acids Res. 25, 51–52.

    Article  PubMed  CAS  Google Scholar 

  • Rogozin, I. B., Makarova, K. S., Murvai, J., Czabarka, E., Wolf, Y. I., Tatusov, R. L., Szekely, L. A. and Koonin, E. V. (2002) Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 30, 2212–2223.

    PubMed  CAS  Google Scholar 

  • Roth, J. R., Benson, N., Galitski, T., Haack, K., Lawrence, J. G. and Miesel, L. (1996) Rearrangements of the Bacterial Chromosome: Formation and Applications. In Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology, 2nd ed. (Neidhardt, F. C., Curtiss III, R., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik, B., Reznikoff, W., Schaechter, M., Umbarger, H. E. and Riley, M., Eds). ASM Press, Chap 120: pp 2256–2276.

    Google Scholar 

  • Salgado, H., Moreno-Hagelsieb, G., Smith, T. F. and Collado-Vides, J. (2000) Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. USA. 97, 6652–6657.

    Article  PubMed  CAS  Google Scholar 

  • Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millán-Zárate, D., Díaz-Peredo, E., Sanchez-Solano, F., Pérez-Rueda, E., Bonavides-Martínez, C., and Collado-Vides, J. (2001) RegulonDB (version 3.2): Transcriptional Regulation and Operon Organization in Escherichia coli K-12 Nucleic Acids. Res. 29, 72–74.

    Article  PubMed  CAS  Google Scholar 

  • Shen-Orr, S. S., Milo, R., Mangan, S. and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 31, 64–68.

    Article  PubMed  CAS  Google Scholar 

  • Snel, B., Bork, P. and Huynen, M. A. (2000) Genome evolution. Gene fusion versus gene fission. Trends Genet. 16, 9–11.

    Article  PubMed  CAS  Google Scholar 

  • Snel, B., Bork, P. and Huynen, M. A. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99, 5890–5895.

    Article  PubMed  CAS  Google Scholar 

  • Snyder, L. and Champness W. (1997) Regulation of Gene Expression. In Molecular Genetics of Bacteria. ASM Press, Washington D.C.

    Google Scholar 

  • Sonnhammer, E. L. L. and Koonin, E. V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18, 619–620.

    Article  PubMed  CAS  Google Scholar 

  • Suyama, M. and Bork, P. (2001) Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17, 10–13.

    Article  PubMed  CAS  Google Scholar 

  • Tamames, J., Casari, G., Ouzounis, C. and Valencia, A. (1997) Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44, 66–73.

    PubMed  CAS  Google Scholar 

  • Tamames, J., González-Moreno, M., Mingorance, J., Valencia, A. and Vicente, M. (2001) Bringing gene order into bacterial shape. Trends Genet. 17, 124–126.

    Article  PubMed  CAS  Google Scholar 

  • Tamames, J. (2001) Evolution of gene order conservation in prokaryotes. Genome Biol. 2, R0020.

    Article  Google Scholar 

  • Tatusov, R. L., Koonin, E. V. and Lipman, D. J. (1997) A genomic perspective on protein families. Science. 278, 631–637.

    Article  PubMed  CAS  Google Scholar 

  • Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., Kiryutin, B., Galperin, M. Y., Fedorova, N. D. and Koonin, E. V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acid Res. 29, 22–28.

    PubMed  CAS  Google Scholar 

  • Thanaraj, T. A. and Argos, P. (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci. 5, 1594–1612.

    PubMed  CAS  Google Scholar 

  • Thieffry, D., Huerta, A. M., Pérez-Rueda, E. and Collado-Vides, J. (1998) From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in E. coli. BioEssays 20, 433–440.

    Article  PubMed  CAS  Google Scholar 

  • Tsoka, S, and Ouzounis, C. A. (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genet. 26, 141–142.

    PubMed  CAS  Google Scholar 

  • Uchiyama, I. (2002) MBGD: microbial genome database for comparative analysis. Nucleic Acid Res. 31, 58–62.

    Google Scholar 

  • Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403, 601–603.

    Google Scholar 

  • Valencia, A., Pazos, F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 10, 368–373.

    Google Scholar 

  • van Noort, V., Snel, B. and Huynen, M.A. (2003) Predicting gene function by conserved coexpression. Trends Genet, 19, 238–242.

    Article  PubMed  CAS  Google Scholar 

  • Vicente, M., Gómez, M. J. and Ayala, A. (1998) Regulation of transcription of cell division genes in E. coli dcw cluster. Cell Mol. Life Sci. 54, 221–271.

    Article  Google Scholar 

  • von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258–61.

    Article  CAS  Google Scholar 

  • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417, 399–403.

    Google Scholar 

  • Watanabe, H., Mori, H., Itoh, T., Gojobori, T. (1997) Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol. 44Suppl 1, S57–64.

    PubMed  CAS  Google Scholar 

  • Wolf, Y. I., Karev, G. and Koonin, E.V. (2002) Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays 24, 105–109.

    Article  PubMed  Google Scholar 

  • Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. and Eisenberg, D. (2002) DIP: The Database of Interacting Proteins. A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303–5.

    Article  PubMed  CAS  Google Scholar 

  • Yada, T., Nakao, M., Totoki, Y. and Nakai, K. (1999) Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics 15, 987–993.

    Article  PubMed  CAS  Google Scholar 

  • Yanai, I. and DeLisi, C. (2002) The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 3, R0064.

    Google Scholar 

  • Yanai, I., Derti, A. and DeLisi, C. (2001) Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. USA. 98, 7940–7945.

    Article  PubMed  CAS  Google Scholar 

  • Yanai, I., Mellor, J. C. and DeLisi, C. (2002) Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 18, 176–179.

    Article  PubMed  CAS  Google Scholar 

  • Yanai, I., Wolf, Y. I. and Koonin, E. V. (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol. 3, R0024.

    Google Scholar 

  • Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M. el al. (2002) MINT: a Molecular INTeraction database. FEBS Letters. 513, 135–140.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, Y. and Cronan, J. E. Jr. (1996) Polar allele duplication for transcriptional analysis of consecutive essential genes: application to a cluster of Escherichia coli fatty acid biosynthetic genes. J. Bacteriol. 178, 3614–3620.

    PubMed  CAS  Google Scholar 

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  1. Protein Design Group, Centre Nacional de Biotecnología, CSIC Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, 28049, Spain

    Manuel J. Gómez, Ildefonso Cases & Alfonso Valencia

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  1. Manuel J. Gómez
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  2. Ildefonso Cases
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  1. CSIC National Biotechnology Centre, Madrid, Spain

    Miguel Vicente , Alfonso Valencia  & Jesús Mingorance ,  & 

  2. BioAlma, S.L., Madrid, Spain

    Javier Tamames

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Gómez, M.J., Cases, I., Valencia, A. (2004). Gene order in Prokaryotes: conservation and implications. In: Vicente, M., Tamames, J., Valencia, A., Mingorance, J. (eds) Molecules in Time and Space. Springer, Boston, MA. https://doi.org/10.1007/0-306-48579-6_11

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